Floods minister Rory Stewart warned there could be a "very bad situation" for flood-hit residents who are due to be hit by a fresh storm and further misery.
He said he is "very concerned" as Storm Frank is due to sweep in from this evening, bringing gales and downpours - with Cumbria and southern and central Scotland most at risk of more disruption.
Most of the nine remaining "severe" flood warnings issued by the Environment Agency(EA) for England and Wales - meaning potential loss of life - are centred on York, which was inundated on Boxing Day.
The storm is looming as a barrier on the River Foss which was opened on Boxing day, flooding hundreds of properties in York, was closed again today after emergency repairs by engineers.
Asked how worried he is about the forecasts for Storm Frank, Mr Stewart told BBC Radio 4's Today programme: "Very concerned. These emergency services personnel have been working really hard, so have volunteers.
"I'm now working my way across Yorkshire, heading back up to Cumbria. People have barely had a break for three and a half weeks because this has been going continually since early December.
"As you say, there's another front coming in, there could be more flooding again so we really need emergency services, voluntary groups, mountain rescue to rest to be ready for what could be a very bad situation Wednesday, Thursday."
On the closure of the River Foss barrier, an EA spokesman said: " We are working round the clock at the Foss barrier to get it back up and running. We are testing the pumps, generators, wiring and barrier so they can work well in conjunction to manage the River Foss levels and protect properties.
"We now have four pumps operating at the barrier. They are running on power from the generators which were dropped onto the roof of the barrier by the Chinook helicopter on Monday.
"From first light this morning, with the help of the military, we will be setting up more generators on site to allow us to get the remaining four pumps back up and running."
The EA's's decision to open the barrier sent flood water coursing through the city streets and left many property owners wondering whether their buildings were put at risk to save others.
The EA said it took this " difficult decision" in a "a rapidly moving situation" to reduce flood risk to the residents of York.
An EA spokesman said: "Had the barrier remained closed, and without the pumps running, the flooding would have been more widespread and many more homes would have flooded. The properties that flooded as a result of the opening of the barrier would have flooded had the barrier remained closed."
Residents were warned before properties flooded, he added.
There has been anger over a perceived North/South divide on flood spending and that flooding in Leeds was a preventable disaster. Mr Stewart rejected that position, telling BBC Breakfast that it is a "very fair system" done on the basis of "how many houses are protected and what the risk is to those properties".
The Met Office said rain overnight would be much lighter than the recent downpours, but Storm Frank - the sixth of the season - would arrive by this evening.
It has issued amber warnings with up to 40mm of persistent rain expected widely across Northern Ireland, west and south-west Scotland, Wales and north-west England - flooded by Storm Desmond - by tomorrow.
Twice that is possible - 80mm - over high ground, with some exposed areas in south-west Scotland and Cumbria warned they could be hit by 100-150mm.
It said the conditions were "not unusual for this time of year" and comparable with the storms of the winter of 2013-14.
Met Office chief meteorologist Will Lang said: "Everyone should be aware of the potential for disruption in places from further flooding and the impacts of the gales to transport."